Real-time LAMP rapid diagnostic method for X. fastidiosa ... · Real-time LAMP rapid diagnostic...
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Real-time LAMP rapid diagnostic method for X. fastidiosa in plant
material and insect vectors
Yaseen Thaer Resercher in CIHEAM Bari, ITALY
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The Need
Ideal diagnostic test suitable for developing should be:
“Reliable” ☻Affordable
☻ Sensitive
☻ Specific
☻ User-friendly
☻ Robust and rapid
☻ Equipment free
☻ Deliverable to the end user
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LAMP (LOOP MEDIATED ISOTHERMAL AMPLIFICATION)
Originally reported by Notomi et al in 2000 of EIKEN Chemical Co. Ltd., Japan
(http://www.eiken.co.jp/en/)
As of 17th May 2017, PubMed database has listed more than 1668 articles on this topic
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4 primers based on the 6 distinct regions of the target gene: the F3c, F2c and F1c regions at the 3' side and the B1, B2 and B3 regions at the 5' side
Design of primers
(http://loopamp.eiken.co.jp/e/lamp/primer.html)
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Bst DNA polymerase with strand displacement activity at
65℃
No need for a step to denature double stranded into a
single stranded form
The amplification efficiency is extremely high
Reduced total cost not require special reagents or
sophisticated equipment
LAMP characteristics
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Amplification specificity is extremely high as LAMP requires 4/6 oligonucleotide primers that recognize 6/8 distinct regions on the target DNA
Detection limit : LAMP ≥ PCR and RT-PCR
Detection time : LAMP < PCR and RT-PCR
LAMP reaction: accelerated by two loop primers
PCR reagent recommended storage temperature is -20oC, LAMP reagents can be stored at 4°C and can shipped at ambient temperature.
Crude DNA preparation can be used as LAMP template DNA.
LAMP vs. PCR
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Examples of LAMP application
Disease Pathogen References
Tomato and potato late blight Phytophthora infestans Hansen et al., 2016
Fusarium wilt of chickpea Fusarium oxysporum f.sp. ciceris Ghosh et al., 2015
Grape powdery Mildew Erysiphe necator Thiessen et al., 2013
Fire blight Erwinia amylovora
Temple and Johnson,
2011; Bühlmann et al.,
2012; Moradi et al., 2012
Citrus Bacterial Canker Xanthomonas spp. Rigano et al., 2010
Grey Mould Botrytis cinerea Tomlinson et al., 2010
Pierce’s disease, citrus veinal
chlorosis, almond leaf scorch,
Olive Quick Decline
Xylella fastidiosa Harper et al., 2010
Yaseen et al., 2015
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Procedure
Nucleic acid extraction
LAMP reaction preparation
Genetic amplification and detection of the results
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START THE APP Sample cutting 4-5 olive leaf peduncle or transfer the insect from 95% alcohol
tube to filter paper, leave them to dry for 5 minutes.
Insert the tube in icgene
Run the extraction procedure for extraction 10’ at 65°C
Run the amplification
Results
Add 22,5ul of LAMP master mix to each primer mix tube + 30ul of mineral oil + 2,5ul of the
extracted DNA of the first step
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SIMPLE AND RAPID DNA EXTRACTION FROM INSECT AND PLANT MATERIAL
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CIHEAM/MAIB Patent number WO2017017555A1
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MONITORING OF XYLELLA FASTIDIOSA IN THE PATHOGEN-FREE AREA USING THE SPY INSECTS APPROACH
Infected zone (red) Buffer zone (blue) Surveillance zone (green) Containment zone (brownish)
Apulia Region Directory 195/2015 - Annex 1
Poster N. 8.6
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Possibility to send the results a real time to a server to collect the data and the all related information
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Sensetivity
10ng
1ng
100pg 1pg
10pg 0,1pg
10ng
1ng
1pg
10pg
0.1pg
10fg
100pg
RT-LAMP
RT-PCR X. fastidiosa DNA
diluted 1:10
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SERIAL DILUTION OF THE PATHOGEN FROM 105 UP TO 10 CELLS
105
104
103 102 10
RT-LAMP
105
104 103
102 10
RT-PCR
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Serial dilutions prepared by spiking a bacterial suspension with an OD600 of 0.5, corresponding to ca. 108 CFU/ml, to get a panel of artificially contaminated samples ranging from 107 to 10 CFU/ml.
ANALYTICAL SENSITIVITY IN THE RING TEST
Technique CONCENTRATION cfu/ml
107 106 105 104 103 102 10
ELISA (Agritest/Loewe)
√ √ √ √
PCR RST31/33
√ √ √ √
qPCR √ √ √ √ √ √
Lamp (enbiotech) on sap
√ √ √ √ √
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User friendly method, easy to handle, only a a simple portable equipment is required;
Ready-to-use extraction system that allows for total DNA extraction in only a few minutes and without the use of sophisticated laboratory instruments
The only method molecular can work with crud extract
Very short time of execution (less than 40 min) including extraction
Its cost is lower than qPCR or the conventional PCR
More sensitive than qPCR
Possibility to send the results a real time to a server to collect the data and the all related information
The only efficient method for on-site detection Xf in the possible vectors and other spy insects which can harbor the bacterium.
REAL TIME LAMP ADVANTAGE
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Possibility of performing genetic tests directly on site
Stable Kit at room temperature, transportation at room temperature and stored at +4°C
Automatic interpretation of results
We recommend the use of RT-LAMP method for insect vector monitoring in buffer and healthy area, as well as for quarantine cross borders control.
REAL TIME LAMP ADVANTAGE
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FAO REGIONAL TCP PROJECT TCP/RAB/3601
Title: Strengthening preventive measures for the introduction and spread of Xylella fastidiosa– Olive Quick Decline Syndrome in NENA countries
Launched in August 2016 in Tunis & still ongoing
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BENEFICIARY COUNTRIES
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Lebanon Palestine
Libya
Morocco
Algeria
Tunisia
Egypt Jordan
Syria
Thank you